!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! VERIFICATION CHECK: vc-memory-leak !!!!! !!!!! !!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Description: Check that the model has no memory leaks. This is tested using the Valgrind memory debugging tool (http://valgrind.org) by performing a series of energy and force calculations on a randomly distorted face-centered cubic (FCC) cube base structure for both non-periodic and periodic boundary conditions. Separate configurations are tested for each species supported by the model, as well as one containing a random distribution of all species. Configurations used for testing are provided as auxiliary files. Author: Ellad Tadmor ----------------------------------------------------------------------------------------------------- Results for KIM Model : EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Au__MO_017524376569_001 Supported species : Au random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 418.38461628000897 Forces: 1 -1.46302705e+01 -3.19907412e+01 -3.26154531e+01 2 -1.92504208e+01 2.55452944e+01 -2.72356575e+01 3 1.32972112e+01 -2.01466828e+01 -2.94435932e+00 4 -2.03609331e+01 2.29585515e+01 1.85075130e+01 5 4.26560988e+00 -5.23942289e+01 -1.36417634e+01 6 2.86341252e+01 1.70432512e+01 -3.16542037e+01 7 2.55377993e+01 -1.03298556e+02 -8.32269525e+01 8 -5.05578914e+01 -3.71133212e+01 -6.45147250e+00 9 -2.50755819e+01 -5.03148618e+01 -7.40266789e+01 10 -8.07515314e+00 6.06542104e+01 -6.92357452e+01 11 -2.36680834e+01 -4.60573899e+01 2.49054675e+01 12 -4.64695941e+01 5.89103878e+01 4.67328415e+01 13 -2.77575564e+01 -4.54349265e+01 -1.38926878e+02 14 2.79757341e+01 3.52197380e+01 -2.56164802e+01 15 1.20954122e+02 -3.48645064e+01 2.11392534e+01 16 1.55288153e+01 9.96311679e+01 4.51321448e+01 17 -6.35602693e+01 -4.43211436e+01 -2.20649195e+01 18 4.80136921e+01 6.18262949e+01 -5.85521173e+01 19 2.15902518e+01 -7.36773741e+01 4.59757688e+01 20 -5.22013061e+01 2.45068519e+01 5.95948138e+01 21 -4.28623124e+01 -3.49707509e+01 2.34886940e+01 22 7.09659564e+01 7.91822140e+01 7.99478020e+01 23 1.67378347e+01 -7.65249360e+00 2.24252510e+01 24 1.82580109e+01 1.64074217e+01 2.55876542e+01 25 -4.71371659e+01 -1.51295032e+01 -1.63005952e+01 26 -1.98976026e+01 6.82133794e+01 -3.26956212e+01 27 5.23570541e+01 -1.10982308e+02 4.94930015e+01 28 -9.89538149e+01 8.95824649e+01 2.49548348e+01 29 -2.52282751e+01 -3.41078691e+01 2.82344355e+01 30 3.56633121e+01 5.60978518e+01 2.91139656e+01 31 5.49517534e+01 -2.37998983e+01 3.68264901e+01 32 3.09549487e+01 5.04774756e+01 5.31289657e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 418.38461628000897 Forces: 1 -1.46302705e+01 -3.19907412e+01 -3.26154531e+01 2 -1.92504208e+01 2.55452944e+01 -2.72356575e+01 3 1.32972112e+01 -2.01466828e+01 -2.94435932e+00 4 -2.03609331e+01 2.29585515e+01 1.85075130e+01 5 4.26560988e+00 -5.23942289e+01 -1.36417634e+01 6 2.86341252e+01 1.70432512e+01 -3.16542037e+01 7 2.55377993e+01 -1.03298556e+02 -8.32269525e+01 8 -5.05578914e+01 -3.71133212e+01 -6.45147250e+00 9 -2.50755819e+01 -5.03148618e+01 -7.40266789e+01 10 -8.07515314e+00 6.06542104e+01 -6.92357452e+01 11 -2.36680834e+01 -4.60573899e+01 2.49054675e+01 12 -4.64695941e+01 5.89103878e+01 4.67328415e+01 13 -2.77575564e+01 -4.54349265e+01 -1.38926878e+02 14 2.79757341e+01 3.52197380e+01 -2.56164802e+01 15 1.20954122e+02 -3.48645064e+01 2.11392534e+01 16 1.55288153e+01 9.96311679e+01 4.51321448e+01 17 -6.35602693e+01 -4.43211436e+01 -2.20649195e+01 18 4.80136921e+01 6.18262949e+01 -5.85521173e+01 19 2.15902518e+01 -7.36773741e+01 4.59757688e+01 20 -5.22013061e+01 2.45068519e+01 5.95948138e+01 21 -4.28623124e+01 -3.49707509e+01 2.34886940e+01 22 7.09659564e+01 7.91822140e+01 7.99478020e+01 23 1.67378347e+01 -7.65249360e+00 2.24252510e+01 24 1.82580109e+01 1.64074217e+01 2.55876542e+01 25 -4.71371659e+01 -1.51295032e+01 -1.63005952e+01 26 -1.98976026e+01 6.82133794e+01 -3.26956212e+01 27 5.23570541e+01 -1.10982308e+02 4.94930015e+01 28 -9.89538149e+01 8.95824649e+01 2.49548348e+01 29 -2.52282751e+01 -3.41078691e+01 2.82344355e+01 30 3.56633121e+01 5.60978518e+01 2.91139656e+01 31 5.49517534e+01 -2.37998983e+01 3.68264901e+01 32 3.09549487e+01 5.04774756e+01 5.31289657e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==20961== Memcheck, a memory error detector ==20961== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==20961== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==20961== Command: python runner2.py EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Au__MO_017524376569_001 ==20961== ==22641== Warning: invalid file descriptor 1048564 in syscall close() ==22641== Warning: invalid file descriptor 1048565 in syscall close() ==22641== Warning: invalid file descriptor 1048566 in syscall close() ==22641== Warning: invalid file descriptor 1048567 in syscall close() ==22641== Use --log-fd= to select an alternative log fd. ==22641== Warning: invalid file descriptor 1048568 in syscall close() ==22641== Warning: invalid file descriptor 1048569 in syscall close() ==22647== Warning: invalid file descriptor 1048564 in syscall close() ==22647== Warning: invalid file descriptor 1048565 in syscall close() ==22647== Warning: invalid file descriptor 1048566 in syscall close() ==22647== Warning: invalid file descriptor 1048567 in syscall close() ==22647== Use --log-fd= to select an alternative log fd. ==22647== Warning: invalid file descriptor 1048568 in syscall close() ==22647== Warning: invalid file descriptor 1048569 in syscall close() ==22770== Warning: invalid file descriptor 1048564 in syscall close() ==22770== Warning: invalid file descriptor 1048565 in syscall close() ==22770== Warning: invalid file descriptor 1048566 in syscall close() ==22770== Warning: invalid file descriptor 1048567 in syscall close() ==22770== Use --log-fd= to select an alternative log fd. ==22770== Warning: invalid file descriptor 1048568 in syscall close() ==22770== Warning: invalid file descriptor 1048569 in syscall close() ==22783== Warning: invalid file descriptor 1048564 in syscall close() ==22783== Warning: invalid file descriptor 1048565 in syscall close() ==22783== Warning: invalid file descriptor 1048566 in syscall close() ==22783== Warning: invalid file descriptor 1048567 in syscall close() ==22783== Use --log-fd= to select an alternative log fd. ==22783== Warning: invalid file descriptor 1048568 in syscall close() ==22783== Warning: invalid file descriptor 1048569 in syscall close() ==22801== Warning: invalid file descriptor 1048564 in syscall close() ==22801== Warning: invalid file descriptor 1048565 in syscall close() ==22801== Warning: invalid file descriptor 1048566 in syscall close() ==22801== Warning: invalid file descriptor 1048567 in syscall close() ==22801== Use --log-fd= to select an alternative log fd. ==22801== Warning: invalid file descriptor 1048568 in syscall close() ==22801== Warning: invalid file descriptor 1048569 in syscall close() ==22805== Warning: invalid file descriptor 1048564 in syscall close() ==22805== Warning: invalid file descriptor 1048565 in syscall close() ==22805== Warning: invalid file descriptor 1048566 in syscall close() ==22805== Warning: invalid file descriptor 1048567 in syscall close() ==22805== Use --log-fd= to select an alternative log fd. ==22805== Warning: invalid file descriptor 1048568 in syscall close() ==22805== Warning: invalid file descriptor 1048569 in syscall close() ==20961== ==20961== HEAP SUMMARY: ==20961== in use at exit: 1,718,292 bytes in 1,321 blocks ==20961== total heap usage: 30,944 allocs, 29,623 frees, 39,187,728 bytes allocated ==20961== ==20961== LEAK SUMMARY: ==20961== definitely lost: 0 bytes in 0 blocks ==20961== indirectly lost: 0 bytes in 0 blocks ==20961== possibly lost: 178,943 bytes in 97 blocks ==20961== still reachable: 1,539,349 bytes in 1,224 blocks ==20961== suppressed: 0 bytes in 0 blocks ==20961== Rerun with --leak-check=full to see details of leaked memory ==20961== ==20961== For counts of detected and suppressed errors, rerun with: -v ==20961== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16344 from 613) ================================================================================ To pass this verification check the number of bytes that are "definitely lost" or "indirectly lost" must be zero. NOTE that Valgrind will typically report non-zero "possibly lost" bytes due to Python's internal memory allocation and garbage collection that it does not monitor. Full Valgrind output written to auxiliary file "valgrind.out" Grade: P Comment: No memory leak detected.